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This commit is contained in:
Greg Von Kuster
2009-01-26 14:41:45 -05:00
parent 95fa32f017 c09f6759ab
commit 66463bea79
2 changed files with 25 additions and 10 deletions
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lib/galaxy/datatypes/data.py
+8 -7
View File
@@ -140,13 +140,14 @@ class Data( object ):
"""Returns formatted html of dataset info"""
try:
# Change new line chars to html
if dataset.info.find( '\r\n' ) >= 0:
dataset.info = dataset.info.replace( '\r\n', '<br/>' )
if dataset.info.find( '\r' ) >= 0:
dataset.info = dataset.info.replace( '\r', '<br/>' )
if dataset.info.find( '\n' ) >= 0:
dataset.info = dataset.info.replace( '\n', '<br/>' )
return escape( dataset.info )
info = escape( dataset.info )
if info.find( '\r\n' ) >= 0:
info = info.replace( '\r\n', '<br/>' )
if info.find( '\r' ) >= 0:
info = info.replace( '\r', '<br/>' )
if info.find( '\n' ) >= 0:
info = info.replace( '\n', '<br/>' )
return info
except:
return "info unavailable"
def validate(self, dataset):
lib/galaxy/tools/actions/__init__.py
+17 -3
View File
@@ -6,6 +6,7 @@ from galaxy.util.none_like import NoneDataset
from galaxy.web import url_for
from galaxy.jobs import JOB_OK
import galaxy.tools
from types import *
import logging
log = logging.getLogger( __name__ )
@@ -68,8 +69,21 @@ class DefaultToolAction( object ):
param_values[input.name] = input_datasets[ prefix + input.name ]
tool.visit_inputs( param_values, visitor )
return input_datasets
def execute(self, tool, trans, incoming={}, set_output_hid=True ):
def make_dict_copy( from_dict ):
"""
Makes a copy of input dictionary from_dict such that all values that are dictionaries
result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle
other complex types ( e.g., lists, etc ), but not sure...
"""
copy_from_dict = {}
for key, value in from_dict.items():
if type( value ).__name__ == 'dict':
copy_from_dict[ key ] = make_dict_copy( value )
else:
copy_from_dict[ key ] = value
return copy_from_dict
def wrap_values( inputs, input_values ):
# Wrap tool inputs as necessary
for input in inputs.itervalues():
@@ -78,7 +92,7 @@ class DefaultToolAction( object ):
wrap_values( input.inputs, d )
elif isinstance( input, Conditional ):
values = input_values[ input.name ]
current = values["__current_case__"]
current = values[ "__current_case__" ]
wrap_values( input.cases[current].inputs, values )
elif isinstance( input, DataToolParameter ):
input_values[ input.name ] = \
@@ -184,7 +198,7 @@ class DefaultToolAction( object ):
data.blurb = "queued"
# Set output label
if output.label:
params = dict( incoming )
params = make_dict_copy( incoming )
# wrapping the params allows the tool config to contain things like
# <outputs>
# <data format="input" name="output" label="Blat on ${<input_param>.name}" />